Compositions and reaction mixtures for the detection of nucleic acids from multiple types of human papillomavirus

ABSTRACT

Nucleic acid oligonucleotide sequences are disclosed which include amplification oligomers and probe oligomers which are useful for detecting multiple types of human papillomaviruses (HPV) associated with cervical cancer. Methods for detecting multiple HPV types in biological specimens by amplifying HPV nucleic acid sequences in vitro and detecting the amplified products are disclosed.

RELATED APPLICATION

This application claims the benefit under 35 U.S.C. 119(e) ofprovisional application No. 60/634,458, filed Dec. 8, 2004, the entirecontents of each of which is incorporated herein by reference in theirentirety.

FIELD OF THE INVENTION

This invention relates to diagnostic detection of infectious agentsassociated with a risk for developing cancer, and specifically relatesto compositions and assays for detecting human papillomavirus (HPV) byusing in vitro nucleic acid amplification and detection assays to detectnucleic acid sequences.

BACKGROUND OF THE INVENTION

Human papillomaviruses (HPV) target epithelial tissues for infection andare etiological agents of a variety of cancers, predominantly squamouscell carcinomas and adenocarcinomas. HPV-associated cancers includethose of the head and neck (larynx, oral cavity, oropharynx, tonsils,and esophagus), respiratory tissue, breast, skin, cervix, and anus.Although HPV infection is considered a necessary factor in developmentof some cancers, other factors may also affect carcinogenesis (Braakhuiset al., 2004, J. Natl. Cancer Inst. 96(13): 998-1006; Dahlstrand et al.,2004, Anticancer Res. 24(3b): 1829-35; Daling et al., 2004, Cancer101(2): 270-80; Ha et al., 2004, Crit. Rev. Oral Biol. Med. 15(4):188-96; Hafkamp et al., Acta Otolaryngol. 124(4): 520-6; Harwood et al.,2004, Br. J. Dermatol. 150(5):949-57; Rees et al., 2004, Clin.Otolaryngol. 29(4):301-6; Widschwendter et al., 2004, J. Clin. Virol.31(4):292-7).

At least 77 different types of HPV have been identified. Of those, HPV16and HPV18 are frequently linked to a variety of HPV-associated cancers,but the risk level associated with a HPV type may vary with differentforms of papilloma-associated cancers. The pathogenesis of humanpapillomaviruses in epithelia has been studied to elucidate the link ofHPV infection to cancers. HPV infect basal layer cells of stratifiedepithelia where they become established as multicopy episomes orintegrated genomes, by which the viral DNA is replicated with cellularchromosomes (reviewed by Longworth et al., 2004, Microbiol. Mol. Biol.Rev. 68(2):362-72). At cell division, a daughter cell migrates away fromthe basal layer and undergoes differentiation in which HPV vegetativeviral replication and late-gene expression are activated to produceprogeny HPV. Although an infected individual's immune system may clearthe HPV infection, usually within 1 to 2 years, infected basal cells maypersist for decades. HPV infection may lead to chromosomal instabilityand aneuploidy that may favor HPV integration (Melsheimer et al., 2004,Clin. Cancer Res. 10(9):3059-63; Reidy et al., 2004, Laryngoscope114(11): 1906-9). During HPV genome integration, the HPV E2 gene may bedestroyed, resulting in deregulated expression of the HPV E6/E7oncogenes that encode oncoproteins that target the regulatory proteinspRb and p53. Thus, a cascade of events that modulate cellular regulationmay result in carcinogenesis (Braun et al., 2004, Cancer Lett.209(1):37-49; Fan et al., 2004, Crit. Rev. Eukaryot. Gene Expr.14(3):183-202; Fiedler et al., 2004, FASEB J. 18(10):1120-2; Psyrri etal., 2004, Cancer Res., 64(9):3079-86; Si et al., 2004, J. Clin. Virol.32(1):19-23).

The association of HPV infection and cervical cancer has been thesubject of considerable research and epidemiological study because ofthe high incidence of cervical cancer worldwide, estimated at 450,000new cases per year. HPV types associated with a high risk of developingcervical cancer (HR-HPV) include HPV types 16, 18, 31, 33, 35, 39, 45,51, 52, 56, 58, 59, 66, 68 and 73, although the epidemiologicalsignificance of individual types may vary with different geographicalregions or clinical testing parameters (Munoz et al., 2004, Int. J.Cancer 111(2): 278-85; Chaturvedi et al., 2005, J. Med. Virol.75(1):105-13; Smith et al., 2004, Int. J. Gynaecol. Obstet.87(2):131-7). HPV infections that are generally considered a low riskfor developing into cervical cancer (LR-HPV) include HPV types 6, 11,43, 43, 44, 61, 71, and 72.

In women infected with HPV, cervical infection may lead to condylomata(genital warts), cervical intraepithelial neoplasia (CIN), and cervicalcancer (Kahn et al., 2004, Adolesc. Med. Clin. 15(2): 301-21, ix).Cytological examination of cervical cells has been the primary screeningtool for detecting cervical cancer in many countries, usually using theCIN grading system (1 to 3) to monitor precancerous lesions fordetermining treatment and/or further monitoring. In addition tocytological screening, molecular screening for HPV nucleic acid may be acost-effective prognostic test that may allow extending the timeinterval between cytological tests (Wiley et al., 2004, Curr. Oncol.Rep. 6(6): 497-506; Zielinski et al., 2004, Obstet. Gynecol. Surv.59(7): 543-53; Clavel et al., 2004, Br. J. Cancer 90(9):1803-8).Molecular assays have been developed for detection of selected HPVproteins and nucleic acid sequences in human biological specimens, e.g.,Pap smears and biopsies (Chen et al., 2005, Gynecol. Oncol.99(3):578-84; Carozzi et al., 2005, Am. J. Clin. Pathol. 124(5): 716-21;Molden et al., 2005, Cancer Epidemiol. Biomarkers Prev. 14(2): 367-72;Asato et al., 2004, J. Infect. Dis. 189(1):1829-32; Federschneider etal., 2004, Am. J. Obstet. Gynecol. 191(3): 757-61; Remmerbach et al., J.Clin. Virol. 30(4):302-8).

Vaccination against common HPV types may be useful to treat or preventgenital warts, condylomata, or prevent development of cancers,particularly cervical cancers. Various forms of HPV vaccinations are indevelopment or testing (Ault et al., 2004, Vaccine 22(23-24):3004-7;Corona Gutierrez et al., 2004, Hum. Genet. Ther. 15(5):421-31; Harper etal., 2004, Lancet 364(9447):1757-65; Roden et al., 2004, Hum. Pathol.35(8):971-82).

There is a need to efficiently and sensitively detect the presence ofHPV in biological specimens to provide diagnostic and prognosticinformation to physicians treating patients infected with HPV,particularly for women whose cervical tissue has been infected withHR-HPV types. There is also a need to efficiently and sensitively detectthe presence of HPV in biological specimens obtained from individualswho have been vaccinated against HPV infection, to determine theshort-term and long-term efficacy of the vaccination.

SUMMARY OF THE INVENTION

This invention includes compositions and methods for detection ofnucleic acid sequences in multiple HPV types that may be present in abiological sample.

According to one aspect of the invention, there is provided a mixture ofamplification oligomers in which individual oligomer sequences areselected from the group consisting of SEQ ID NO:18 to SEQ ID NO:42,which includes the complementary oligomer sequences or RNA equivalentsof the specified sequences. A preferred embodiment of the mixtureincludes first amplification oligomers of SEQ ID Nos. 19 or 42, 21, 23,25, 27, 29, 31, 33 and 35, and second amplification oligomers of SEQ IDNos. 37, 38, 39, 40 and 41, or complementary oligomer sequences or RNAequivalents of the oligomer sequences. Another preferred embodimentincludes first amplification oligomers of SEQ ID Nos. 18, 20, 22, 24,26, 28, 30, 32, 34 and 36, and second amplification oligomers of SEQ IDNos. 37, 38, 39, 40 and 41, or complementary oligomer sequences or RNAequivalents of the oligomer sequences. Another preferred embodimentincludes first amplification oligomers of SEQ ID Nos. 19 or 42, 21, 23,25, 27, 29, 31, 33 and 35, and second amplification oligomers of SEQ IDNos. 38, 39, 40 and 41, or complementary oligomer sequences or RNAequivalents of the oligomer sequences. Another preferred embodimentincludes first amplification oligomers of SEQ ID Nos. 18, 20, 22, 24,26, 28, 30, 32, 34 and 36, and second amplification oligomers of SEQ IDNos. 38, 39, 40 and 41, or complementary oligomer sequences or RNAequivalents of the oligomer sequences. In some embodiments of themixture of oligomers, one or more individual oligomers include abackbone that includes at least one 2′-methoxy RNA group, at least one2′ fluoro-substituted RNA group, at least one peptide nucleic acidlinkage, at least one phosphorothioate linkage, at least onemethylphosphonate linkage, or any combination thereof. Embodiments ofthe mixtures may be contained in a kit.

According to another aspect of the invention, there is provided amixture of oligomers in which individual oligomer sequences are selectedfrom the group consisting of SEQ ID NO:11 to SEQ ID NO:17, SEQ ID NO:44to SEQ ID NO:54 and SEQ ID NO:58, which includes the complementaryoligomer sequences or RNA equivalents of the specified sequences. Apreferred embodiment of the mixture includes SEQ ID Nos. 11 to 17, orcomplementary oligomer sequences or RNA equivalents of the oligomersequences. Another preferred embodiment includes SEQ ID Nos. 11 to 15and 17, or complementary oligomer sequences or RNA equivalents of theoligomer sequences. Another preferred embodiment includes SEQ ID Nos. 11to 15 and 17 and at least one oligomer of SEQ ID NO:44 to SEQ ID NO:54and SEQ ID NO:58, or complementary oligomer sequences or RNA equivalentsof the oligomer sequences. Another preferred embodiment includes SEQ IDNos. 11, 12, 14, 15, 17, 44, 45 and 52, or complementary oligomersequences or RNA equivalents of the oligomer sequences. Preferredembodiments of the mixture include those in which each oligomer sequenceincludes a label joined directly or indirectly to the oligomer. In somepreferred embodiments, each oligomer sequence includes a label that is achemiluminescent compound, which is more preferably an acridinium ester(AE) compound. In some preferred embodiments of the mixture, eacholigomer sequence has a backbone comprising at least one 2′-methoxy RNAgroup. Embodiments of these mixtures may be contained in a kit.

According to another aspect of the invention, there is provided amixture of at least two oligomers in which individual oligomer sequencesare selected from the group consisting of SEQ ID Nos. 1 to 10, whichincludes the complementary oligomer sequences or RNA equivalents of thespecified sequences. A preferred embodiment of the mixture includes atleast two oligomers selected from SEQ ID Nos. 2, 4, 6, 8 and 10 with aligand moiety joined to each oligomer. Another preferred embodimentincludes a mixture of oligomers of SEQ ID Nos. 2, 4, 6, 8 and 10 with aligand moiety joined to each oligomer. Another preferred embodiment ofthe mixture includes at least two oligomers selected from SEQ ID Nos. 1,3, 5, 7 and 9. Another preferred embodiment of the mixture includesoligomers of SEQ ID Nos. 1, 3, 5, 7 and 9. In some preferredembodiments, at least one oligomer has a backbone that includes at leastone 2′-methoxy RNA group, at least one 2′ fluoro-substituted RNA group,at least one peptide nucleic acid linkage, at least one phosphorothioatelinkage, or at least one methylphosphonate linkage. Preferredembodiments of the mixtures are contained in a kit.

According to another aspect of the invention, there is provided a methodof detecting human papillomavirus (HPV) nucleic acid present in abiological sample that includes the steps of: contacting nucleic acid ina biological sample containing RNA of at least one of HPV types 16, 18,31, 33, 35, 39, 45, 51, 52, 56, 58, 59 and 68 with a mixture ofamplification oligomers that amplify a HPV sequence in an E6/E7 targetregion sequence, in which the mixture is made up of first amplificationoligomers and second amplification oligomers for amplifying the HPVtarget region sequences of the multiple types; amplifying a HPV sequencefrom the target region sequence in at least one HPV type by using theamplification oligomers and a nucleic acid polymerase in vitro toproduce an HPV amplified product; and detecting the amplified product byusing a detection probe oligomer that is sufficiently complementary tohybridize specifically with the HPV amplified product to indicate thepresence in the sample of at least one of HPV types 16, 18, 31, 33, 35,39, 45, 51, 52, 56, 58, 59 and 68. In a preferred embodiment, theamplifying step uses first amplification oligomers of SEQ ID Nos. 19 or42, 21, 23, 25, 27, 29, 31, 33 and 35, and second amplificationoligomers of SEQ ID Nos. 37, 38, 39, 40 and 41, or complementaryoligomer sequences or RNA equivalents of the oligomer sequences. Anotherpreferred embodiment in the amplifying step uses first amplificationoligomers of SEQ ID Nos. 18, 20, 22, 24, 26, 28, 30, 32, 34 and 36, andsecond amplification oligomers of SEQ ID Nos. 37, 38, 39, 40 and 41, orcomplementary oligomer sequences or RNA equivalents of the oligomersequences. One preferred embodiment in the amplifying step uses firstamplification oligomers of SEQ ID Nos. 19 or 42, 21, 23, 25, 27, 29, 31,33 and 35, and second amplification oligomers of SEQ ID Nos. 38, 39, 40and 41, or complementary oligomer sequences or RNA equivalents of theoligomer sequences. Another preferred embodiment in the amplifying stepuses first amplification oligomers of SEQ ID Nos. 18, 20, 22, 24, 26,28, 30, 32, 34 and 36, and second amplification oligomers of SEQ ID Nos.38, 39, 40 and 41, or complementary oligomer sequences or RNAequivalents of the oligomer sequences. A preferred embodiment of themethod further includes a step of separating RNA of at least one of HPVtypes 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59 and 68 from othercomponents in the sample by contacting HPV RNA in the sample with acapture oligomer and separating a complex that includes the captureoligomer and HPV RNA from other components in the sample before theamplifying step. In a preferred embodiment that includes the separatingstep, the capture oligomer is present in a mixture of capture oligomersmade up of at least two oligomers in which individual oligomer sequencesare selected from the group consisting of SEQ ID Nos. 1 to 10, whichincludes the complementary oligomer sequences or RNA equivalents of thespecified sequences. In preferred embodiments of the method that includethe separating step, the capture oligomer is present in a mixture ofcapture oligomers made up of at least two oligomers selected from SEQ IDNos. 2, 4, 6, 8 and 10 with a ligand moiety joined to each oligomer; oroligomers of SEQ ID Nos. 2, 4, 6, 8 and 10 with a ligand moiety joinedto each oligomer; or at least two oligomers selected from SEQ ID Nos. 1,3, 5, 7 and 9; or oligomers of SEQ ID Nos. 1, 3, 5, 7 and 9. In apreferred embodiment of the method, the amplifying step uses anamplification process that is substantially isothermal. A preferredembodiment of the method uses a transcription-associated amplificationmethod in the amplifying step. One embodiment of the method in thedetecting step uses a mixture of probe oligomers in which at least oneprobe oligomer binds specifically to the HPV amplified product andresults in a signal to indicate the presence in the sample of at leastone of the HPV types. In a preferred embodiment, the detecting step usesa mixture of probe oligomers made up of SEQ ID Nos. 11 to 17, orcomplementary oligomer sequences or RNA equivalents of the oligomersequences. Another preferred embodiment in the detecting step uses amixture of probe oligomers made up of SEQ ID Nos. 11 to 15 and 17, orcomplementary oligomer sequences or RNA equivalents of the oligomersequences. Another preferred embodiment in the detecting step uses amixture of probe oligomers made up of SEQ ID Nos. 11 to 15 and 17 and atleast one oligomer of SEQ ID NO:44 to SEQ ID NO:54 and SEQ ID NO:58, orcomplementary oligomer sequences or RNA equivalents of the oligomersequences. Another preferred embodiment in the detecting step uses amixture of probe oligomers made up of SEQ ID Nos. 11, 12, 14, 15, 17,44, 45 and 52, or complementary oligomer sequences or RNA equivalents ofthe oligomer sequences. One embodiment of the method further amplifiesand detects a non-HPV internal control sequence. In a preferredembodiment that includes an internal control, the contacting stepfurther includes introducing a non-HPV internal control sequence intothe sample, the amplifying step further includes amplifying the non-HPVinternal control sequence to produce an amplified internal controlsequence, and the detecting step further includes detecting theamplified internal control sequence to produce a signal that indicatesthat the method steps have been performed appropriately.

The following description and accompanying drawing, which is part of thespecification, serve to explain and illustrate the principles of theinvention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a drawing of a phylogenetic tree showing the geneticrelatedness of some HPV types.

DETAILED DESCRIPTION OF THE INVENTION

This invention includes oligomer sequences and methods for detectingnucleic acid sequences from multiple HPV types (16, 18, 31, 33, 35, 39,45, 51, 52, 56, 58, 59, 66, and 68) present in biological samplesderived from humans. These sequences and methods are useful fordiagnosis of HPV infections, including persistent infections for whichdetection of HPV sequences provides prognostic information related tocarcinogenesis. The sequences and assays are also useful for monitoringthe status of a patient at risk for cancer, and/or for assessing andmonitoring a patient's response to a therapeutic treatment. Because theassays sensitively detect the presence of HPV nucleic acids, they arealso useful for detecting vascular space invasion or lymph nodemetastases of HPV-associated cancers, thus providing further prognosticinformation. The sequences and assays are also useful for monitoring theefficacy of anti-HPV vaccination in individuals exposed to HPV aftervaccination.

The targeted HPV types cumulatively represent high-risk types associatedwith cervical cancer. The oligomer sequences were designed to preferablydetect more than one HPV type within the group by targeting E6/E7 genesequences that are common or very similar between different HPV types,while avoiding adverse interactions between oligonucleotides that mayoccur when they are present in a mixture, such as an in vitro nucleicacid amplification reaction or a hybridization detection reaction. Thesequences were also designed to avoid detecting related sequences foundin HPV types that are characterized as low-risk for cervical cancer(e.g., HPV types 6, 11, 42, 43 and 44). Different HPV types were groupedbased on their genetic relatedness, as shown in FIG. 1, for comparisonsof target sequences, and are referred to herein as group A1 thatincludes HPV types 16, 31, and 35, group A2 that includes HPV types 33,52, and 58, group B that includes HPV types 6, 11, 42, 43 and 44, groupC1 that includes HPV types 18, 45, and 59, and group D that includes HPVtypes 51, 56 and 66. For comparison of sequences, known sequencesobtained from a publicly available database (GenBank) were alignedeither manually or by using a computerized algorithm and oligonucleotidesequences were selected for synthesis and testing by using the alignedsequences to suggest likely oligomers that fit a variety of criteria,including sequence length in a range of about 15 to 30 nt, GC content,and predicted Tm of a hybridization complex that includes the selectedsequence, and a substantial lack of predictable secondary structure dueto self-hybridization or intermolecular hybridization with otherselected oligomers. Selected sequences were designed to specificallyrecognize the target HPV genomic or RNA sequence of one, or preferablymore than one, HPV type within a group under substantially the samehybridization conditions for all of the selected oligonucleotidesequences. Known sequences used in alignments and selections includedGenBank accession numbers AF092932, AF125673, AF404678, D90400, J04353,K02718, M12732, M27022, M73236, M14119, M62849, M74117, X05015, X74477,X74479, X74481, X74483, X77858, and Y13218. From the selected sequences,oligomers were synthesized in vitro using standard methods, and thesynthetic oligomers were characterized, e.g., by experimentallydetermining T_(m) of a hybridization complex that includes the oligomerand usually a synthetic RNA sequence that contains the complement of theoligomer sequence, and for their functional characteristics in nucleicacid amplification and detection reactions using conditions previouslydescribed in detail (e.g., U.S. Pat. Nos. 5,399,491 and 5,554,516,Kacian et al., and U.S. Pat. No. 5,283,174, Arnold et al.). For use insuch methods, the HPV-specific sequences may be joined to additionalsequences, e.g., with a 5′ promoter sequence as shown in SEQ ID Nos. 18,20, 22, 24, 26,28, 30, 32, 34 and 36, or with a 3′ tail sequence asshown in SEQ ID Nos. 1, 3, 5, 7 and 9.

To select oligomers efficiently that functioned in an assay to detectmany different HPV types, the following process was used. First,oligomers to serve as detection probes for the HPV groups were selected,which determined the target area of the HPV genomic or RNA sequences tobe amplified. Then, amplification oligomers were selected for each ofthe candidate target regions, synthesized, and tested in amplificationreactions with individual HPV types of a group to be detected (e.g., HPV16, 31 and 35 in group A1). If amplification and detection reactionsproduced substantially similar positive results for each HPV type in agroup, then the oligomers for different groups (e.g., A1 and A2) werecombined in multiplex amplification and detection reactions and testedfor each of the HPV types in the combined groups to determine if theoligomer mixture functioned properly to provide positive results foreach of the HPV types in the combined groups, or whether adverseinteractions (e.g., between oligomers in the mixture) resulted indecreased assay sensitivity or specificity. If assay results in themultiplex format were unacceptable, one or more oligomers wereredesigned, synthesized and tested in substantially the same manner.This process was reiterated for various combinations of oligomers toobtain combinations of oligomers that functioned in a multiplex assay toamplify and detect HPV types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58,59, 66, and 68. Further optimization of the multiplex assay was achievedby using empirically determined optimal amounts of the oligomers in amixture to produce positive results for each of the target HPV sequenceswhile minimizing interfering interactions between the oligomers.

Selected oligomer sequences used to amplify and detect the multiple HPVtypes' sequences are summarized in Table 1. The HPV group designationsfor the sequences provided for convenience and it will be understoodthat an oligomer sequence may also functionally recognize HPV sequencesof a type in another group in a multiplex reaction. Sequences in Table 1are shown as DNA sequences, but it will be understood that theseembodiments also encompass sequences consisting of their correspondingRNA sequences, and sequences that are completely complementary to thedisclosed DNA sequences or their corresponding RNA sequences.

TABLE 1 SEQ NO: Group Sequence  1 A1gctcataacagtggaggtcagttgcctctttaaaaa aaaaaaaaaaaaaaaaaaaaaaaaa  2 A1gctcataacagtggaggtcagttgcctc  3 A2 ctccaacacgctgcacagcgccctgtttaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa  4 A2 ctccaacacgctgcacagcgccctg  5 C1gtgcacagatcaggtagcttgtagggtcgtttaaaa aaaaaaaaaaaaaaaaaaaaaaaaaa  6 C1gtgcacagatcaggtagcttgtagggtcg  7 C2 gcacaggtctggcaatttgtatggccgtttaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa  8 C2 gcacaggtctggcaatttgtatggccg  9 Dggtctttgacatctgtgacaccttattttaaaaaaa aaaaaaaaaaaaaaaaaaaaaaa 10 Dggtctttgacatctgtgacaccttat 11 A1 cagctggacaagcagaaccggac 12 A2ggccagatggacaagcacaac 13 C1 tgtgtgtgtgttgtaagtgt 14 C2ccgaccatgcagttaatcacc 15 D gcgtgaccagctaccagaaag 16 Dgccacagcaagctagacaagc 17 D cacgtaccttgttgtgagtg 18 A1aatttaatacgactcactatagggagagaagcgtag agtcacacttgcaac 19 A1agcgtagagtcacacttgcaac 42 A1 gaagcgtagagtcacacttgcaac 20 A1aatttaatacgactcactatagggagacacacaaac gaagtgtagacttacactgac 21 A1cacacaaacgaagtgtagacttacactgac 22 A1aatttaatacgactcactatagggagagtgtcgcct cacatttacaacaggacg 23 A1gtgtcgcctcacatttacaacaggacg 24 A2 aatttaatacgactcactatagggagagttacaatgtagtaatcagctgtggc 25 A2 gttacaatgtagtaatcagctgtggc 26 A2aatttaatacgactcactatagggagacacaatgta gtaattacttgtggc 27 A2cacaatgtagtaattacttgtggc 28 C1 aatttaatacgactcactatagggagagcacaccacggacacacaaagga 29 C1 gcacaccacggacacacaaagga 30 C1aatttaatacgactcactatagggagaggatagtgt gtccataaacagctgctg 31 C1ggatagtgtgtccataaacagctgctg 32 C2 aatttaatacgactcactatagggagaccgtctggctagtagttgatg 33 C2 ccgtctggctagtagttgatg 34 Daatttaatacgactcactatagggagaccactgcca gttgtactacacttgaac 35 Dccactgccagttgtactacacttgaac 36 D aatttaatacgactcactatagggagactctgaatgtccaactgcaccacaaac 37 D ctctgaatgtccaactgcaccacaaac 38 A1,gtgacagctcagatgaggatg A2 39 C1 cgacgagccgaaccac 40 C2gaccttgtatgtcacgagc 41 D gacagctcagaggaggaggatg 44 C1gtagtagaaagctcagcagacgacc 45 C1 gtagagagctcggcagaggac 46 C1gtagagagctcggcagaigac (wherein ″i″ is inosine) 47 C1gaccttagaacactacagcagc 48 C1 gtgtgacggcagaattgagc 49 C1cttcagctagtagtagaaacctcgc 50 C1 cagctagtagtagaaacctcgcaagac 51 C1agctagtagtagaaacctcgcaagacgg 52 C1 gtagtagaaacctcgcaagacgg 53 C1gtagaaacctcgcaagacgg 54 C1 gcaagacggattgcgagcct 58 Dgagcaatttgacagctcagagg

As described below, some of these oligomers are preferably used asamplification oligomers which include embodiments referred to aspromoter primers, some are preferably used as detection probes, and someare preferably used as capture probe oligomers to facilitate separationof HPV nucleic acid from other components of a biological sample beforeamplification of the HPV target sequence. Capture probe oligomerspreferably target sequences in E6/E7 gene sequences, whereasamplification and detection oligomers preferably target E7 genesequences. These oligomer sequences and methods that use them are usefulfor detecting many different HPV types that are associated with anincreased risk of developing cancer in humans. They are useful fordetecting expression of HPV genes E6 and E7, which, when constitutivelyexpressed in human cells, lead to cell cycle deregulation and cellproliferation that may progress to cancer. Because HPV E6/E7 geneexpression is suppressed in cells that harbor episomal HPV, the assayand oligomer components was designed to detect E6/E7 RNA present in abiological sample to provide prognostic information by detecting HPVexpression associated with neoplasia and carcinogenesis.

To aid in understanding the invention and its preferred embodiments, thefollowing definitions are provided. Other scientific and technical termsused herein have the same meaning as commonly understood by thoseskilled in the relevant art. General definitions of terms may be foundin, e.g., Dictionary of Microbiology and Molecular Biology, 2nd ed.(Singleton et al., 1994, John Wiley & Sons, New York, N.Y.) or TheHarper Collins Dictionary of Biology (Hale & Marham, 1991, HarperPerennial, New York, N.Y.). Unless otherwise described, the techniquesemployed or contemplated herein are standard methodologies that are wellknown to one of ordinary skill in the art.

A “biological sample” refers to any tissue or material derived from aliving or dead human which may contain the target nucleic acid,including, for example, samples of larynx, oral cavity, oropharynx,tonsil, or esophagus tissue, respiratory tissue or exudates, cervical oranal swab samples, biopsy tissue including lymph nodes, gastrointestinaltissue, feces, urine, semen, sputum, peripheral blood, plasma, serum orother body fluids, tissues or materials. A biological sample may betreated to physically or mechanically disrupt tissue or cell structureto release intracellular components into a solution which may furthercontain enzymes, buffers, salts, detergents and the like, using wellknown methods.

“Nucleic acid” refers to a multimeric compound (oligomer or polymer)comprising nucleosides or nucleoside analogs which have nitrogenousbases, or base analogs, and which are linked together by phosphodiesterbonds or other known linkages to form a polynucleotide. Nucleic acidsinclude conventional ribonucleic acid (RNA), deoxyribonucleic acid(DNA), or chimeric DNA-RNA, and analogs thereof. A nucleic acid“backbone” may be made up of a variety of linkages, including one ormore of sugar-phosphodiester linkages, peptide-nucleic acid bonds (in“peptide nucleic acids” or PNAs, see PCT No. WO 95/32305, Hydig-Hielsenet al.), phosphorothioate linkages, methylphosphonate linkages, orcombinations thereof. Sugar moieties of the nucleic acid may be eitherribose or deoxyribose, or similar compounds having known substitutions,e.g., 2′ methoxy substitutions and 2′ halide substitutions (e.g., 2′-F).Nitrogenous bases may be conventional bases (A, G, C, T, U), analogsthereof (e.g., inosine; The Biochemistry of the Nucleic Acids 5-36,Adams et al., ed., 11^(th) ed., 1992), derivatives of purine orpyrimidine bases (e.g., N⁴-methyl deoxyguanosine, deaza- or aza-purines,deaza- or aza-pyrimidines, pyrimidine bases having substituent groups atthe 5 or 6 position, purine bases having an altered or replacementsubstituent at the 2, 6 and/or 8 position, such as2-amino-6-methylaminopurine, O⁶-methylguanine, 4-thio-pyrimidines,4-amino-pyrimidines, 4-dimethylhydrazine-pyrimidines, andO⁴-alkyl-pyrimidines, and pyrazolo-compounds, such as unsubstituted or3-substituted pyrazolo[3,4-d]pyrimidine; U.S. Pat. Nos. 5,378,825,6,949,367 and PCT No. WO 93/13121). Nucleic acids may include “abasic”residues in which the backbone does not include a nitrogenous base forone or more residues (U.S. Pat. No. 5,585,481, Arnold et al.). A nucleicacid may comprise only conventional sugars, bases, and linkages as foundin RNA and DNA, or may include conventional components and substitutions(e.g., conventional bases linked by a 2′ methoxy backbone, or a nucleicacid including a mixture of conventional bases and one or more baseanalogs). Nucleic acids also include “locked nucleic acids” (LNA), ananalogue containing one or more LNA nucleotide monomers with a bicyclicfuranose unit locked in an RNA mimicking sugar conformation, whichenhances hybridization affinity toward complementary sequences insingle-stranded RNA (ssRNA), single-stranded DNA (ssDNA), ordouble-stranded DNA (dsDNA) (Vester et al., 2004, Biochemistry43(42):13233-41). Synthetic methods for making nucleic acids in vitroare well known in the art.

The interchangeable terms “oligomer” and “oligonucleotide” refer to anucleic acid having generally less than 1,000 residues, including thosein a size range having a lower limit of about 2 to 5 nucleotides.Preferred oligomers fall in a size range having a lower limit of about 5to about 15 nucleotides and an upper limit of about 60 to 150nucleotides. More preferably, oligomers are in a size range of about 15to 100 nucleotides. Oligomers may be purified from naturally occurringsources, but preferably are synthesized by using any known enzymatic orchemical methods.

An “amplification oligonucleotide” or “amplification oligomer” refers toan oligomer that hybridizes to a target nucleic acid, or its complement,and participates in an in vitro nucleic acid amplification reaction. Anamplification oligomer may be referred to as a “primer” or “promoterprimer.” Generally, a primer hybridizes to a template nucleic acidstrand and has a 3′ end that is extended in a polymerization reaction toproduce a complementary strand to the template strand. The 5′ region ofa primer may be non-complementary to the target nucleic acid, e.g., itmay contain a 5′ promoter sequence and the oligomer is referred to as apromoter primer. Those skilled in the art will appreciate that anyoligomer that has a target-complementary sequence and functions as aprimer can be modified to include a 5′ promoter sequence, and thusfunction promoter primer. Similarly, a promoter primer can function as aprimer independent of its promoter sequence. Preferred embodiments ofamplification oligonucleotides contain at least 10 contiguous bases, andmore preferably at least 12 contiguous bases, that are complementary toa target sequence (or a complementary strand thereof). The contiguousbases are preferably at least about 80%, more preferably at least about90%, and most preferably about 100% complementary to the target regionto which the oligomer hybridizes. An amplification oligomer ispreferably about 10 to about 65 nucleotides long and may includemodified nucleotides or base analogs.

“Amplification” refers to an in vitro method for obtaining multiplecopies of a target sequence, its complement, or fragments of a targetsequence. Amplification of “fragments” refers to production of anamplified nucleic acid that contains less than the complete targetregion sequence or its complement. For example, a complete gene may bereferred to as a target sequence for an assay, but amplification maymake copies of a smaller sequence (e.g., about 85 to 200 nucleotides)contained in the target gene sequence. Known amplification methodsinclude, e.g., transcription-associated amplification,replicase-mediated amplification, the polymerase chain reaction (PCR),ligase chain reaction (LCR), and strand-displacement amplification(SDA). Replicase-mediated amplification uses self-replicating RNAmolecules, and a replicase such as QB-replicase (U.S. Pat. No.4,786,600, Kramer et al.). PCR amplification uses DNA polymerase,primers and thermal cycling to synthesize multiple copies of twocomplementary strands of DNA or cDNA (U.S. Pat. Nos. 4,683,195,4,683,202, and 4,800,159, Mullis et al., and Methods in Enzymology,1987, Vol. 155: 335-350). LCR amplification uses at least four separateoligonucleotides to amplify a target and its complementary strand byusing multiple cycles of hybridization, ligation, and denaturation(e.g., U.S. Pat. No. 5,427,930, Birkenmeyer et al., U.S. Pat. No.5,516,663, Backman et al., and EP Pat. App. No. 0 320 308). SDA uses aprimer that contains a recognition site for a restriction endonucleasesuch that the endonuclease will nick one strand of a hemimodified DNAduplex that includes the target sequence, followed by amplification in aseries of primer extension and strand displacement steps (e.g., U.S.Pat. No. 5,422,252, Walker et al., U.S. Pat. No. 5,547,861, Nadeau etal., U.S. 5,648,211, Fraiser et al.). Transcription-associatedamplification is a preferred embodiment described below. It will beapparent to one skilled in the art that the oligonucleotides and methodsillustrated by the preferred embodiments may be readily adapted to usein any primer-dependent amplification system by one skilled in the artof molecular biology.

“Transcription-associated amplification” or “transcription-mediatedamplification” (TMA) refer to any type of nucleic acid amplificationthat uses an RNA polymerase to produce multiple RNA transcripts from anucleic acid template. These methods generally employ an RNA polymerase,a DNA polymerase, deoxyribonucleoside triphosphates, ribonucleosidetriphosphates, and a template complementary oligonucleotide thatincludes a promoter sequence, and optionally may include one or moreother oligonucleotides. Variations of transcription-associatedamplification are well known in the art as disclosed in detailpreviously (U.S. Pat. Nos. 5,399,491 and 5,554,516, Kacian et al.; U.S.Pat. No. 5,437,990, Burg et al.; PCT Nos. WO 88/01302 and WO 88/10315,Gingeras et al.; U.S. Pat. No. 5,130,238, Malek et al.; U.S. Pat. Nos.4,868,105 and 5,124,246, Urdea et al.; PCT No. WO 95/03430, Ryder etal.; and U.S. patent application Ser. No. 11/213,519, Becker et al.,filed Aug. 26, 2005). The TMA methods of Kacian et al. are preferredembodiments of amplification methods used for detection of targetsequences as described below. Although preferred embodiments areillustrated by using TMA or transcription-associated amplification, aperson of ordinary skill in the art will appreciated that amplificationoligomers disclosed herein may be readily applicable to use in otheramplification methods based on polymerase-mediated extension of oligomersequences.

A “detection probe” refers to a nucleic acid oligomer that hybridizesspecifically to a target sequence in a nucleic acid, preferably in anamplified sequence, under conditions that promote hybridization, toallow detection of the target sequence or amplified nucleic acid.Detection may either be direct (i.e., resulting from a probe hybridizingdirectly to the target or amplified nucleic acid) or indirect (i.e.,resulting from a probe hybridizing to an intermediate molecularstructure that links the probe to the target or amplified nucleic acid).A probe's “target” generally refers to a sequence within (i.e., a subsetof) an amplified nucleic acid sequence which hybridizes specifically toat least a portion of a probe oligomer using standard hydrogen bonding(base pairing), although a probe sequence does not have to be 100%complementary to the target sequence. Sequences that are “sufficientlycomplementary” allow stable hybridization of a probe oligomer to atarget sequence that is not completely complementary to the probe'starget-specific sequence. In addition to its target-specific sequences,a probe may include other sequences that contribute to itsthree-dimensional conformation or detection function (e.g., U.S. Pat.Nos. 5,118,801 and 5,312,728, Lizardi et al.; U.S. Pat. Nos. 6,849,412,6,835,542, 6,534,274, and 6,361,945, Becker et al.).

By “sufficiently complementary” is meant a contiguous nucleic acidsequence that is capable of hybridizing to another sequence by hydrogenbonding between a series of complementary bases, which may becomplementary at each position in the sequence by using standard basepairing (e.g., G:C, A:T or A:U pairing) or may contain one or morenon-complementary residues so long as the entire sequence is capable ofspecifically hybridizing with another sequence in appropriatehybridization conditions. Contiguous bases are preferably at least about80%, more preferably at least about 90%, and most preferably about 100%complementary to a sequence to which an oligomer is intended tospecifically hybridize. Appropriate hybridization conditions are wellknown to those skilled in the art, can be predicted readily based onsequence composition, or can be determined empirically by using routinetesting (e.g., Sambrook et al., Molecular Cloning, A Laboratory Manual,2^(nd) ed. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor,N.Y., 1989) at §§1.90-1.91, 7.37-7.57, 9.47-9.51 and 11.47-11.57particularly at §§9.50-9.51, 11.12-11.13, 11.45-11.47 and 11.55-11.57).

A “capture probe” or “capture oligomer” refers to at least one nucleicacid oligomer that provides a means for specifically joining a targetsequence to a support to separate the target nucleic acid from othercomponents in a mixture. A capture oligomer may rely on any known ligandinteraction to link the target to a support, and preferred embodimentslink the target to an immobilized oligomer on a support by using basepair hybridization. Embodiments of capture oligomers may include twobinding regions: a target sequence-binding region and an immobilizedprobe-binding region, usually on the same oligomer, although the regionsmay be present on two different oligomers joined together by one or morelinkers. An “immobilized probe” refers to a nucleic acid that joins,directly or indirectly, a capture oligomer to an immobilized support. Animmobilized oligomer joined to a solid support facilitates separation ofthe bound target sequence from unbound material in the mixture. Anyknown solid support may be used, e.g., matrices or particles insolution, made of any known support material, e.g., nitrocellulose,nylon, glass, polyacrylate, mixed polymers, polystyrene, silanepolypropylene and metal particles, preferably, magnetically attractableparticles. Preferred target capture materials and methods have beenpreviously described in detail (U.S. Pat. Nos. 6,110678 and 6,280,952,Weisburg et al.).

By “separating” or “purifying” is meant that one or more components of abiological sample are removed from one or more other components of thesample. For example, sample components include nucleic acids in agenerally aqueous solution that may include other materials such asproteins, carbohydrates, lipids and cellular organelles or debris.Preferably, a separating or purifying step removes at least about 70%,more preferably at least about 90% and, even more preferably, at leastabout 95% of the other components present in the sample from the desiredtarget.

A “label” refers to a molecular moiety or compound that can be detectedor can lead to a detectable response. A label can be joined directly orindirectly to a nucleic acid probe. Direct labeling can occur throughbonds or interactions that link the label to the probe, includingcovalent bonds or non-covalent interactions, e.g., hydrogen bonding,hydrophobic and ionic interactions, or formation of chelates orcoordination complexes. Indirect labeling can occur through use of abridging moiety or “linker” which is/are either directly or indirectlylabeled, and which may amplify a detectable signal. Labels can be anyknown detectable moiety, e.g. radionuclides, ligands, enzyme or enzymesubstrate, reactive group, or chromophore, such as a dye, bead, orparticle that imparts a detectable color, luminescent compounds (e.g.,bioluminescent, phosphorescent or chemiluminescent labels) andfluorescent compounds. Preferably, the label on a labeled probe isdetectable in a homogeneous assay system, i.e., bound labeled probe in amixture containing unbound probe exhibits a detectable change, such asstability or differential degradation, compared to unbound probe. Apreferred label for use in a homogenous assay is a chemiluminescentcompound, and preferred chemiluminescent labels are acridinium ester(“AE”) compounds, that include standard AE or derivatives thereof (e.g.,naphthyl-AE, ortho-AE, 1- or 3-methyl-AE, 2,7-dimethyl-AE,4,5-dimethyl-AE, ortho-dibromo-AE, ortho-dimethyl-AE, meta-dimethyl-AE,ortho-methoxy-AE, ortho-methoxy(cinnamyl)-AE, ortho-methyl-AE,ortho-fluoro-AE, 1- or 3-methyl-ortho-fluoro-AE, 1- or3-methyl-meta-difluoro-AE, and 2-methyl-AE) (U.S. Pat. No. 5,656,207,Woodhead et al.; U.S. Pat. No. 5,658,737, Nelson et al.; and U.S. Pat.No. 5,639,604, Arnold, Jr., et al.). Synthesis and methods of attachinglabels to nucleic acids and detecting labels are well known (seeSambrook et al., Molecular Cloning, A Laboratory Manual, 2nd ed. (ColdSpring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989), Chapter10; U.S. Pat. No. 5,658,737, Nelson et al.; U.S. Pat. No. 5,656,207,Woodhead et al.; U.S. Pat. No. 5,547,842, Hogan et al.; U.S. Pat. No.5,283,174, Arnold et al.; U.S. Pat. No. 4,581,333, Kourilsky et al.; andEuropean Pat. App. Pub. No. 0 747 706, Becker et al.).

By “consisting essentially of” is meant that additional component(s),composition(s) or method step(s) that do not materially change theability to detect the specified multiple HPV target sequences of any oneor all of groups A1, A2, C1, C2, and D by using an in vitroamplification reaction using embodiments of the disclosed amplificationoligomers and detection by using embodiments of the disclosed detectionprobes may be included in the compositions, kits, or methods of thepresent invention. Any component(s), composition(s), or method step(s)that interfere with the ability of these materials or procedures todetect the specified multiple HPV target sequences of any one of groupsA1, A2, C1, C2, and D by using in vitro amplification and detectionreactions would fall outside of this term.

The present invention includes compositions (nucleic acid captureoligomers, amplification oligomers and probes) and methods for detectingHPV nucleic acid in a human biological sample. To select oligomersequences appropriate for use as capture probes, amplificationoligomers, and detection probes, known HPV RNA or DNA sequences of 31different known subtypes (including partial sequences) available frompublicly accessible databases (e.g., GenBank) were aligned by matchingregions of the same or similar sequences in the E6/E7 gene sequences andcompared by using well known molecular biology techniques. Additionalfeatures considered in designing the oligomers included the relative GCcontent of the sequence, the relative absence of predicted secondarystructure (e.g., hairpin turns forming intramolecular hybrids), therelative absence of predicted intermolecular interactions when theoligomers were present in a mixture under hybridization conditions,using methods well known in the art. Although such comparisons andpredictions may be facilitated by the use of computerized algorithms,those skilled in the art can readily perform such comparisons manually.The HPV E6/E7 sequences were compared and sequences of closely relatedtypes with substantial sequence similarity were segregated into thegroups A1, A2, B, C1, C2, and D. Sequence comparisons were made bothwithin the closely related groups and between groups and portions ofE6/E7 sequences that contained relatively few sequence variants within agroup (i.e., consensus regions) were identified and chosen as a basisfor designing synthetic oligomers suitable hybridization to targetsequences in one or more HPV types. By designing oligomers for consensussequences, instead of combinations of amplification and detectionoligomers specific for each individual HPV type to be detected, thetotal number of oligomers in a reaction mixture is reduced, thusreducing the probability of unintended oligomer interactions that areknown to occur in amplification reactions (e.g., formation of “primerdimers” or non-target amplification products), and also reducingbackground signals which are generally proportional to the number ofdetection probes used in a single reaction. Oligomers based on usingconsensus sequences, however, are generally more difficult to designbecause the target regions available for designing consensus sequencesmay be more limited and some of the designed oligomers may not becompletely complementary to one or more of the intended targetsequences. That is, for one or more of the HPV types to be detected byusing these combinations of oligomers, one or more mismatches may occurbetween an oligomer sequence and its intended complementary targetsequence for one or more of the HPV types in a group. Also, an oligomermay be a complete match to one HPV type's target sequence in a group(e.g., HPV16 in group A1) and contain mismatch(es) to other HPV types inthe group (e.g., HPV 31 and/or 35), but still function in amplifyingand/or detecting the types in the group. Similarly, an oligomer designedto function for one group (e.g., an amplification oligomer for group A2)may function in combination with other amplification oligomers toamplify sequences in multiple types of more than one group (e.g., typesin groups A1 and A2). Based on these considerations, amplificationoligomers were designed to hybridize to HPV gene sequences (sense strandor the complementary strand sequence) in the E7 gene, generally toamplify sequences of about 80 to about 150 nucleotides (e.g.,embodiments amplified sequences of 107 nt for HPV16, 152 nt for HPV18,118 nt for HPV31, 82 nt for HPV33, 109 nt for HPV35, 96 nt for HPV39,152 nt for HPV45, 133 nt for HPV51, 86 nt for HPV52, 146 nt for HPV56,83-85 nt for HPV58, 132 nt for HPV59, and 99 nt for HPV68). Detectionprobes were designed to hybridize to a target sequence contained withinthe amplified sequence made by using the corresponding set of primers,i.e., to detect a sequence between the target sequences of a particularset of primers. The target regions for designing capture probe oligomersgenerally were located in the E6/E7 gene sequences 5′ to the targetsequences for amplification of an HPV type or group. In many cases,reiterations of redesign and empirical testing were performed tooptimize selection of the oligomers presented in Table 1.

Embodiments of capture probe oligomers include those of SEQ ID Nos. 1 to10, with preferred embodiments including a substantially homopolymeric3′ tail region (T₃A₃₀), as shown in SEQ ID Nos. 1, 3, 5, 7, and 9.

Embodiments of detection probe oligomers include those of SEQ ID Nos.11to 17, 41, 44 to 54, and 58. From about 50 designs that were synthesizedas oligomers and tested, preferred probe oligomers had a size range of20 to 23 nt, a GC content in a range of about 40 to 50%, and anestimated melting temperature (T_(m)) in the range of about 55° C. to70° C. Embodiments of probe oligomers were synthesized and labeled withan AE chemiluminescent compound (e.g., 2-methyl-AE) by using anon-nucleotide linker moiety and methods previously described in detail(U.S. Pat. Nos. 5,185,439, 5,585,481, and 5,656,744, Arnold Jr. et al.,and U.S. Pat. No. 5,639,604, Arnold et al., see column 10, line 6 tocolumn 11, line 3, and Example 8). Preferred labeling positions occur ina central region of an oligomer, near a region of A/T base pairs, at a3′ or 5′ terminus, or at or near a mismatch site with a known non-targetsequence to be avoided in detection. Embodiments of AE-labeled probesinclude those labeled at the following positions: between nt 4 and 5 forSEQ ID Nos. 15 and 53, between nt 5 and 6 for SEQ ID Nos. 11, 14, 17,44, 50 and 52, between nt 7 and 8 for SEQ ID Nos.15, 17, 47, 48, 52 and54, between nt 8 and 9 for SEQ ID Nos. 12, 14, 41, 45, 47, 49, 54 and58, between nt 9 and 10 for SEQ ID Nos. 47 and 48, between nt 10 and 11for SEQ ID Nos. 17, 44 and 47, between nt 11 and 12 for SEQ ID Nos. 13,44, 45, 46, 47, 50, 51 and 53, between nt 12 and 13 for SEQ ID Nos. 13,15, 51 and 53, between nt 13 and 14 for SEQ ID Nos. 14, 16, 45, 47 and54, between nt 14 and 15 for SEQ ID Nos. 13, 14, 49 and 52, between nt15 and 16 for SEQ ID Nos. 13 and 52, between nt 16 and 17 for SEQ IDNO:44, between nt 17 and 18 for SEQ ID Nos. 44, 47 and 58, between nt 19and 20 for SEQ ID NO:51, between nt 20 and 21 for SEQ ID NO:50, andbetween nt 21 and 22 for SEQ ID NO:44. Preferred embodiments includeAE-labeled probes labeled at the following positions: between nt 5 and 6for SEQ ID NO:11, between nt 7 and 8 for SEQ ID Nos.15, and 17, betweennt 8 and 9 for SEQ ID NO:12, between nt 10 and 11 for SEQ ID NO:44,between nt 11 and 12 for SEQ ID NO:45, between nt 13 and 14 for SEQ IDNO:14, and between nt 14 and 15 for SEQ ID NO:52. Preferred embodimentsof detection probes were synthesized as sequences of RNA bases linked by2′ methoxy backbones. Probe embodiments of SEQ ID Nos. 49 to 54cumulatively target the sequence of SEQ ID NO:55, and overlapping probesof SEQ ID Nos. 49 to 53 all include the sequence of SEQ ID NO:56.

Embodiments of these detection probes include mixtures of probes thatdetect HPV sequences in the multiple HPV types contained in groups A1,A2, C2, C2 and D, i.e., HPV types 16, 31, 35, 33, 52, 58, 18, 45, 59,39, 68, 51 and 56. A preferred embodiment of such a mixture is made upof detection probes of SEQ ID Nos. 11 to 15 and 17. A particularlypreferred embodiment is a mixture of AE-labeled probes of SEQ ID NO:11labeled between nt 5 and 6, SEQ ID NO:12 labeled between nt 8 and 9, SEQID NO:13 labeled between nt 15 and 16, SEQ ID NO:14 labeled between nt13 and 14, SEQ ID NO:15 labeled between nt 7 and 8, and SEQ ID NO:17labeled between nt 7 and 8. Another preferred embodiment of such amixture is made up of probes of SEQ ID Nos. 11, 12, 14, 15, 17, 44, 45and 52. A particularly preferred embodiment is a mixture of AE-labeledprobes of SEQ ID NO:11 labeled between nt 5 and 6, SEQ ID NO:12 labeledbetween nt 8 and 9, SEQ ID NO:14 labeled between nt 13 and 14, SEQ IDNO:15 labeled between nt 7 and 8, SEQ ID NO:17 labeled between nt 7 and8, SEQ ID NO:44 labeled between nt 10 and 11, SEQ ID NO:45 labeledbetween nt 11 and 12, and SEQ ID NO:52 labeled between nt 14 and 15.Those skilled in the art will appreciate that detection probes may beused to detect HPV types of individual groups, e.g., HPV types in groupA1, A2, C1, C2, or D, or combinations of related types, such as those ingroups A1 and A2. Preferred embodiments of such detection probesidentified by their respective target groups include those of SEQ IDNO:11 for group A1, SEQ ID NO:12 for group A2, SEQ ID NO:13 or a mixtureof SEQ ID Nos. 44, 45 and 52 for group C1, SEQ ID NO:14 for group C2,and SEQ ID Nos. 15 and 17 for group D.

Embodiments of amplification oligomers include those of SEQ ID Nos. 18to 42. Some embodiments contain only sequences that target HPVsequences, i.e., those of SEQ ID Nos. 19, 21, 23, 25, 27, 29, 31, 33,35, 37, 38, 39, 40, 41, and 42, whereas others contain additionalfunctional sequences, i.e., promoter sequences. Embodiments of promoterprimers that include the promoter sequence of SEQ ID NO:43 at the 5′ endof the oligomer includes those of SEQ ID Nos. 18, 20, 22, 24, 26, 28,30, 32, 34, and 36. Sequences that are structurally related asHPV-specific sequences and promoter primers that include a 5′ promotersequence attached to the HPV-specific sequence are the following: SEQ IDNos. 19 and 18, SEQ ID Nos. 42 and 18, SEQ ID Nos. 21 and 20, SEQ IDNos. 23 and 22, SEQ ID Nos. 25 and 24, SEQ ID Nos. 27 and 26, SEQ IDNos. 29 and 28, SEQ ID Nos. 31 and 30, SEQ ID Nos. 33 and 32, SEQ IDNos. 35 and 34, and SEQ ID Nos. 37 and 36. Preferred mixtures orcombinations of amplification oligomers for amplifying sequences of theHPV types by groups include those of: SEQ ID NO:18 or 19, SEQ ID NO:20or 21, and SEQ ID NO:22 or 23, with SEQ ID NO:38 for group A1, SEQ IDNO:24 or 25, and SEQ ID NO:26 or 27, with SEQ ID NO:38 for group A2, SEQID NO:28 or 29, and SEQ ID NO:30 or 31, with SEQ ID NO:39 for group C1,SEQ ID NO:32 or 33 with SEQ ID NO:40 for group C2, and SEQ ID NO:34 or35, and SEQ ID NO:36 or 37, with SEQ ID NO:41 for group D. Preferredembodiments use a mixture of amplification oligomers that togetheramplify sequences from HPV types 16, 31, 35, 33, 52, 58, 18, 45, 59, 39,68, 51 and 56 (i.e., HPVs contained in all of groups A1, A2, C1, C2 andD). One preferred embodiment of such a mixture of amplificationoligomers for HPV types 16, 31, 35, 33, 52, 58, 18, 45, 59, 39, 68, 51and 56 include those of SEQ ID Nos. 18, 20, 22, 24, 26, 28, 30, 32, 34,36, 38, 39, 40, and 41. Another preferred embodiment of such a mixtureof amplification oligomers for HPV types 16, 31, 35, 33, 52, 58, 18, 45,59, 39, 68, 51 and 56 include those of SEQ ID Nos.19, 21, 23, 25, 27,29, 31, 33, 35, 37, 38, 39, 40, and 41.

The assay to detect multiple HPV sequences in a biological sampleincludes the steps of amplifying at least one HPV nucleic acid sequenceof an E6/E7 target region from an HPV type contained in HPV group A1,A2, C1, C2, or D by using at least two amplification oligomers asprimers to produce an amplified nucleic acid, preferably in atranscription-associated amplification reaction, and detecting theamplified nucleic acid by hybridizing it with a detection probe sequencethat is sufficiently complementary to a sequence contained in theamplified nucleic acid. A preferred embodiment uses a mixture ofamplification oligomers of SEQ ID Nos. 18, 20, 22, 24, 26, 28, 30, 32,34, 36, 38, 39, 40, and 41 in the amplification reaction that is atranscription-associated amplification reaction. Another preferredembodiment uses a mixture of amplification oligomers of SEQ ID Nos. 19,21, 23, 25, 27, 29, 31, 33, 35, 37, 38, 39, 40, and 41 in theamplification reaction. The amplified nucleic acid is detected bydetecting a signal that results from binding the detection probespecifically to an amplified sequence, even though such specific bindingmay not result from hybridization of sequences in the amplified nucleicacid that are completely complementary to the detection probe sequence.Detecting a signal may result from instances in which the amplifiedsequence is unlabeled and is bound to a labeled detection probe, inwhich the bound labeled detection probe provides a detectable signal.Detecting a signal may result from instances in which the amplifiednucleic acid is bound to an unlabeled probe, followed by detection ofthe complex that includes the amplified nucleic acid and the probe, suchas by detecting a signal resulting from formation of the hybridizationcomplex made up of the detection probe and the amplified nucleic acid,e.g., an electrical signal. Preferred embodiments use detection probesof SEQ ID Nos. 11 to 17, labeled with a chemiluminescent compound.Preferred embodiments use a mixture of detection probes that detectamplified HPV sequences of HPV types 16, 31, 35, 33, 52, 58, 18, 45, 59,39, 68, 51 and 56. A preferred embodiment of a probe mixture used fordetection is made up of probes of SEQ ID Nos. 11 to 15 and 17, morepreferably labeled with a chemiluminescent label. Another preferredembodiment of a probe mixture used for detection is a mixture ofAE-labeled probes of SEQ ID Nos.11 to 15 and 17. Another preferredembodiment of a probe mixture used for detection is made up of probes ofSEQ ID Nos. 11, 12, 14, 15, 17, 44, 45 and 52, more preferably labeledwith a chemiluminescent label. Another preferred embodiment of a probemixture for detection is a mixture of AE-labeled probes of SEQ ID Nos.11, 12, 14, 15, 17, 44, 45 and 52. Additional embodiments of the assaymay use detection probes to detect HPV types of individual groups, suchas in confirmatory assaying of the amplified nucleic acid sequences todetect HPV types in group A1, A2, C1, C2, or D, or combinations of HPVtypes, such as those in groups A1 and A2. Preferred embodiments of suchassays use detection probes of SEQ ID NO:11 for detection of HPV typesin group A1, SEQ ID NO:12 for detection of HPV types in group A2, SEQ IDNO:13 or a mixture of SEQ ID Nos. 44, 45 and 52 for detection of HPVtypes in group C1, SEQ ID NO:14 for detection of HPV types in group C2,or SEQ ID Nos. 15 and 17 for detection of HPV types in group D.

Another embodiment of the assay uses two amplification and detectionreactions for each biological sample tested. The first reaction includesa mixture of amplification oligomers that can amplify the HPV types ingroups A1, A2, C1, C2, or D, to produce at least one amplified HPVsequence from at least one of the HPV types. The second reactionincludes a mixture of amplification oligomers to amplify sequences ofboth HPV types 16 and 18. The amplified products of the twoamplification reactions then are detected separately. For the firstamplification reaction, the amplified products are detected with amixture of detection probes that detect HPV types of groups A1, A2, C1,C2, and D, to detect the presence of at least one of those HPV types inthe sample. For the second amplification reaction, the amplifiedproducts are detected with a mixture of detection probes specific fordetection of HPV 16 and HPV 18 amplified sequences, to detect thepresence of HPV16, HPV18, or both types in the sample. This assayprovides additional diagnostic information because when the firstamplification and detection reactions provide a positive result, thenthe sample contained any one of the HPV types of groups A1, A2, C1, C2,and D. If the second amplification and detection reactions also providea positive result, then the tested sample contained at least one of themost commonly found HR-HPV type(s), HPV 16 and/or HPV 18. If the firstreaction provides a positive result and the second reaction provides anegative result, then a HR-HPV type is present in the sample, but it isnot HPV16 or HPV 18. Based on such information, medical personnel mayselect the appropriate follow-up monitoring for such a patient.Embodiments of the assay use in the first reaction a mixture ofamplification oligomers of SEQ ID Nos. 18, 20, 22, 24, 26, 28, 30, 32,34, 36, 38, 39, 40, and 41, or a mixture of amplification oligomers ofSEQ ID Nos. 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 38, 39, 40, and 41,and amplified products are detected with a mixture of probe oligomers ofSEQ ID Nos. 11 to 15 and 17 or a mixture made up of probes of SEQ IDNos. 11, 12, 14, 15, 17, 44, 45 and 52. In the second reaction for HPV16and HPV18 detection, a mixture of amplification oligomers of SEQ ID Nos.18, 28, and 39, or a mixture of amplification oligomers of SEQ ID Nos.19, 29, and 39 are used in the amplifying step, and the detecting stepuses a mixture of detection probes of SEQ ID Nos. 11 and 13. Anotherassay embodiment for a single sample includes three reactions: a firstreaction to amplify and detect any one of the HPV types of groups A1,A2, C1, C2, and D as described above, a second reaction to amplify anddetect specifically only HPV 16 sequences, and a third reaction toamplify and detect specifically only HPV 18 sequences. This three-partassay provides significant diagnostic information on the types of HPVnucleic acid present in the sample by using relatively few reactions.

The assays for HPV detection may also include a step of isolating orpurifying a target HPV RNA before the amplification step by using acapturing step. Preferred embodiments use a mixture of capture probeoligomers under hybridizing conditions, one portion of a captureoligomer specifically hybridizes to an HPV E6/E7 target sequence of atleast one HPV type of groups A1, A2, C1, C2, or D and another portion ofthe capture oligomer serves as one of a binding pair (ligand) toimmobilize the captured HPV RNA on a solid support to facilitateseparation of the captured HPV RNA from other sample components beforethe amplification step. One or more of the amplification oligomers usedin the subsequent amplification reaction may be included in the HPVcapturing step because the amplification oligomers hybridize to separatetarget sequences than those of the capture probe oligomers in the HPVRNA and do not interfere with target capture but provide a primer on thetarget for the initiation of the amplification reaction. A preferredembodiment uses a mixture of capture probes that include SEQ ID Nos. 2,4, 6, 8, and 10. Other preferred embodiments use a mixture of captureprobe oligomers that include the HPV-specific sequences of SEQ ID Nos.2, 4, 6, 8, and 10 covalently linked to a 3′ tail portion, as in amixture of capture probes of SEQ ID Nos. 1, 3, 5, 7, and 9. TheHPV-specific sequence of the capture probe hybridizes to the HPV targetsequence and the tail portion hybridizes to a complementary sequence(oligo-dT) that is immobilized to a solid support. Preferably, thehybridizations of the capture step are performed with the captureoligomer and HPV target RNA free in solution to utilize thehybridization kinetics associated with solution phase nucleic acidhybridization. This hybridization produces a capture oligomer:HPV RNAcomplex that is then bound to an immobilized probe by hybridization ofthe tail portion of the capture oligomer with its complementaryimmobilized sequence and the resulting complex is separated from othersample components by using standard methods (e.g., filtration,centrifugation, magnetic separation). It will be understood by thoseskilled in the art that any binding pair ligand or set of complementarysequences between the tail portion and the immobilized probe may be usedto perform the capture step. In preferred embodiments, the immobilizedprobe is oligo-dT attached to magnetically attractable monodisperseparticles so that hybridization complexes containing HPV RNA are readilyseparated from solution by applying magnetic force to the vesselcontaining the reaction mixture. The captured HPV target RNA may bewashed one or more times, further purifying the target from potentialinhibitors (e.g., by resuspending particles with attached HPVRNA:capture oligomer:immobilized probe complexes in a washing solutionand retrieving the particles with the attached complexes from thewashing solution). To limit the number of handling steps, the HPV targetnucleic acid may be amplified without releasing it from the captureoligomer. If amplification oligomers are present during the targetcapture step, then the initial amplification reaction (cDNA formation)may be accomplished by polymerization from the 3′ ends of theamplification oligomers hybridized to the captured HPV target RNA.

Assays for HPV detection may optionally include a non-HPV internalcontrol (IC) nucleic acid that is amplified and detected in the sameassay reaction mixtures by using amplification and detection oligomersspecific for the IC sequence that react under the same assay conditionsto provide a positive signal that is distinguishable from anHPV-associated signal (e.g., a different AE label is used for theIC-specific probe compared to the HPV probes and the distinguishablesignals are detected separately using well known methods (e.g., U.S.Pat. Nos. 5,658,737, 5,756,706, 5,827,656 and 5,840,873, Nelson et al.).Amplification and detection of a signal from the amplified IC sequencedemonstrates that the assay reagents, conditions, and performance ofassay steps were properly used in the assay if no signal is obtained forthe HPV target (e.g., samples that test negative for the presence ofHPV). The IC may be used as an internal calibrator for the assay when aquantitative result is desired, i.e., the signal obtained from the ICamplification and detection is used to set a parameter used in analgorithm for quantitating the amount of HPV nucleic acid in a samplebased on the signal obtained for amplified HPV target sequences. Apreferred embodiment of an IC is a randomized sequence that has beenderived from a naturally occurring source (e.g., an HIV sequence thathas been rearranged in a random manner). A preferred IC is an RNAtranscript synthesized in vitro, e.g. transcripts made from a clonedrandomized sequence, to provide an accurate amount of IC per reaction.Primers and a probe specific for the IC target sequence synthesized invitro and used to amplify the IC target sequence and detect theamplified IC sequence by using substantially the same assay conditionsused to amplify and detect the HPV sequences. In preferred embodimentsthat include a target capture step, the assay further includes a captureprobe specific for the IC target in the same capture step used to purifythe HPV targets, so that the IC is treated at every step in the assay inthe assay in a manner analogous to that for the HPV analytes.

Amplifying the captured HPV target region can be accomplished using avariety of known nucleic acid amplification reactions, but preferablyuses a transcription-associated amplification reaction. In such anembodiment, many strands of nucleic acid are produced from a single copyof target nucleic acid, thus permitting detection of the target bydetecting probes that are bound to the amplified sequences.Transcription-associated amplification is performed at substantiallyisothermal conditions as described in detail previously (e.g.,transcription mediated amplification (TMA) as described by Kacian et al.in U.S. Pat. Nos. 5,399,491 and 5,554,516, and nucleic acidsequence-based amplification (NASBA) as described by Davey et al. inU.S. Pat. No. 5,409,818). Briefly, transcription-associatedamplification uses a promoter primer that contains a target-specificsequence and a promoter sequence for an RNA polymerase, another primer,enzymes to supply synthetic and degradative activities (reversetranscriptase (RT), DNA-dependent RNase, and RNA polymerase), substrates(deoxyribonucleoside triphosphates, ribonucleoside triphosphates) andappropriate salts, buffers, and cofactors in solution to producemultiple RNA transcripts from a nucleic acid template. Briefly, apromoter primer hybridizes specifically to its target RNA sequence andreverse transcriptase creates a first strand cDNA by extension from the3′ end of the promoter primer. The cDNA may be made available forhybridization with the second primer by using any method (e.g,denaturing the duplex), but preferably uses RNase H activity (e.g.,supplied by RT enzyme) that digests the RNA strand in the cDNA:RNAduplex. The second primer binds to the cDNA and a new strand of DNA issynthesized from the 3′ end of the second primer by using RT to create adouble-stranded DNA having a functional promoter sequence at one end.RNA polymerase binds to the promoter sequence and transcribes multipletranscripts (“amplicons”). These amplicons are used in subsequent stepsof the amplification process, each serving as a template for a new roundof replication to generate large amounts of amplified nucleic acid(about 100 to 3,000 copies synthesized from each RNA template strand).

A promoter primer oligonucleotide contains a 5′ promoter sequence thatserves as a functional promoter when bound by the appropriate RNApolymerase, and a 3′ sequence that hybridizes specifically to a targetregion sequence. Preferred embodiments include a T7 promoter sequencespecific for T7 RNA polymerase. Preferred embodiments of promoterprimers include those of SEQ ID Nos. 18, 20, 22, 24, 26, 28, 30, 32, 34,and 36, which are used in combination with primers of SEQ ID Nos. 38 to41.

In transcription-mediated amplification of HPV sequences, the HPV RNA ishybridized to a promoter primer, e.g., one or more of SEQ ID Nos. 18,20, 22, 24, 26, 28, 30, 32, 34, and 36, and by using the RT activity, acDNA is synthesized from the promoter primer using the HPV RNA as thetemplate. Then, the second primer, e.g., one or more of SEQ ID Nos. 38to 41, hybridizes to the cDNA strand and RT-mediated polymerizationforms a DNA duplex, thus forming a functional double-stranded promoterwhich bound by its specific RNA polymerase that transcribes RNAtranscripts from the HPV sequence, making HPV amplification products. Byrepeating the hybridization and polymerization steps following the cDNAsynthesis step, additional RNA transcripts are produced, thus producingHPV target-specific amplification products.

It will be appreciated that other in vitro nucleic acid amplificationsystems that use amplification oligomers (e.g., PCR or SDA) may be usedto amplify the HPV target sequences, and these do not require a promotersequence on a primer. For such amplification methods, preferred mixturesof amplification oligomers use first primer oligomers of SEQ ID Nos. 19,21, 23, 25, 27, 29, 31, 33, 35, and 37 with second primer oligomers ofSEQ ID Nos. 38 to 41.

The detecting step generally uses a mixture of HPV-specific probes fordetection of any one of the target HPV types which may be present in thesample, i.e., when at least one probe binds specifically to an amplifiedHPV sequence (e.g., RNA transcripts or amplicons) a positive result isobtained. For assays that detect HPV types of groups A1, A2, C1, C2, andD, the detecting step uses a mixture of detection probes, preferably amixture of SEQ ID Nos. 11 to 15 and 17 or SEQ ID Nos. 11, 12, 14, 15,17, 44, 45 and 52. In assays that involve two or three amplification anddetection reactions to detect the presence of any one of HPV types ofgroups A1, A2, C1, C2, and D on one reaction and to detect a subset ofthe HPV types such as HPV 16 and/or HPV 18 in another reaction, a singleprobe or subset of the probe mixture is used in the detecting step forthe subset of the HPV types (e.g., SEQ ID NO:11, SEQ ID NO:13, or SEQ IDNO:44, individually or as a mixture of SEQ ID NO:11 and SEQ ID No. 13 or44). Preferred embodiments use a labeled probe that produces a signalthat is detected without purifying bound from unbound probes (i.e., in ahomogeneous detection system). More preferably, the probe is labeledwith an acridinium ester (AE) compound to produce a detectablechemiluminescent signal (U.S. Pat. Nos. 5,283,174 and 5,656,744, Arnoldet al.; U.S. Pat. No. 5,658,737, Nelson et al.).

For the methods described herein, the capture oligomers, amplificationoligomers and detection probes oligomers have specific sequences thathave been identified as useful for detecting multiple types of HPVtarget sequences localized in the E6/E7 gene regions of HPV types16, 18,31, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 68. Many oligomers weredesigned to hybridize to more than one HPV type in a genetically relatedgroup by selecting target sequences that are common to multiple HPVtypes or by creating consensus sequences that include common structuralfeatures of multiple HPV types but are not identical to all types, oreven one type, in the targeted group. Embodiments of amplificationoligomers are those of SEQ ID Nos. 18 to 42, and embodiments ofdetection probe oligomers are those of SEQ ID Nos. 11 to 17, 41, 44 to54, and 58. For probes labeled with chemiluminescent compounds,additional oligomers that are substantially complementary to the probeoligomer may be hybridized to the probe oligomer to stabilize thelabeled probe during storage, and embodiments of such probe protectionoligomers are those of SEQ ID Nos. 59 to 64. Preferred embodiments ofcapture probe oligomers have the HPV target-binding sequences of SEQ IDNos. 2, 4, 6, 8 and 10, which may be attached to any moiety that canserve as a binding partner (i.e., ligands such as biotin or avidin) forlinking the target region sequences to a retrievable solid phase.Embodiments of capture probes may include a tail sequence thathybridizes to an immobilized complementary oligomer, as in those of SEQID Nos. 1, 3, 5, 7, and 9, which include a 3′ tail sequence of dT₃A₃₀.These oligomers have generally been disclosed as contiguous DNAsequences, but it will be appreciated that their RNA equivalentsequences, or similar sequences that contain substitutions at one ormore positions of base analogs (e.g., inosine) or synthetic purine andpyrimidine derivatives, such as P or K bases (Lin & Brown, 1989, Nucl.Acids Res. 17:10373-83; Lin & Brown, 1992, Nucl. Acids Res. 20:5149-52), may function in substantially the same way. For oligomers thatbind to RNA targets, embodiments may contain a 2′-methoxy backbone atone or more linkages in the nucleic acid backbone. Preferred embodimentssynthesized with a 2′-methoxy backbone generally use RNA bases forpositions linked by the 2′-methoxy backbone.

Embodiments of the invention include kits made up of variouscombinations of materials useful for performing the method steps fordetection of HPV nucleic acids in a specimen. Preferred kits contain aamplification oligonucleotides that serve as primers for in vitroamplification of nucleic acid sequences of HPV types of groups A1, A2,C1, C2 and D. Exemplary kits include a first and a second amplificationoligonucleotides that are complementary to opposite strands of the HPVtarget sequences and flank the ends of the HPV sequence to be amplified.Embodiments include amplification oligomers that contain the sequencesof SEQ ID Nos. 18 or 19, 20 or 21, 22 or 23, 24 or 25, 26 or 27, 28 or29, 30 or 31, 32 or 33, 34 or 35, and 36 or 37 as a first amplificationoligomer, and sequences of SEQ ID Nos. 38 to 41 as the secondamplification oligomer. The first amplification oligonucleotide ispreferably up to 100 nt in length, more preferably is from 20 to 60 ntin length, in which the nucleotide bases complementary to the HPV targetregion sequence may include substitutions of one or more base analogs.The second amplification oligonucleotide is preferably up to 100 nt inlength, more preferably is from about 15 to 25 nt in length, which mayinclude of one or more nitrogenous base analogs. Kit embodiments mayfurther contain one or more probe oligomers for detecting the HPVamplified products. Embodiments of these probes include oligomers of 11to 17, 44 to 54 and 58, and preferably use probes of SEQ ID Nos. 11, 12,14, 15, 17, 44, 45 and 52. Kits embodiments may further includeadditional oligomers, such as those of SEQ ID Nos. 57 and 59 to 64,packaged in a mixture with probe oligomers to stabilize functionalcomponents of the probe oligomers before use. Kits may also containoligomers that serve as capture oligomers for purifying the targetnucleic acid from a sample. Examples of capture oligomers for use inkits include those that contain about 25 to 30 nt complementary to HPVtarget sequences in the HPV E6/E7 gene region in HPV types of groups A1,A2, C1, C2 and D. Embodiments of capture oligomers included in kitspreferably include those that contain the HPV-specific sequences of SEQID Nos. 2, 4, 6, 8, and 10 attached to a ligand that binds the captureoligomer to a solid support. Preferred embodiments of capture oligomersin kits include a mixture of oligomers of SEQ ID Nos. 1, 3, 5, 7 and 9,which include a substantially homopolymeric tail sequence attached tothe 3′ end of the HPV-specific sequences of SEQ ID Nos. 2, 4, 6, 8, and10. It will be understood that embodiments of the kits described aboveembrace kits in which the oligomers consist of the complementarysequences of the specified sequences, RNA and DNA equivalents or RNA/DNAchimerics of the specified sequences, or substantially equivalentsequences that may contain one or more substitutions of nucleotideanalogs in the specified sequences. It will also be understood that kitembodiments may include oligomers as individually packaged components,but preferably include mixtures of oligomers, e.g., a mixture of targetcapture and first amplification oligomers, or a mixture of probeoligomers. Kits useful for practicing the methods of the invention mayinclude those that include any of the amplification oligomers and/ordetection probes disclosed herein which are packaged in combination witheach other. Kits may also include capture oligomers which may bepackaged in combination with the amplification oligonucleotides and/ordetection probes. Kits for practicing the methods of the invention mayfurther include one or more reagents for use in methods steps of targetcapture, in vitro amplification, and/or detection of amplified productsas described herein. It will be clear to those skilled in the art, thatthe present invention embraces many different kit configurations.

Oligomers described herein have been tested in assays that captured HPVRNA from samples by using a target capture step, amplified the capturedHPV target sequences in a transcription-mediated amplification reaction,and detected the amplified sequences by using labeled detection probesin a homogeneous reaction to detected a chemiluminescent signal frombound probes to indicate the presence of HPV in the tested sample. Thegeneral method steps used in these assays have been described previously(U.S. Pat. Nos. 6,110,678, 6280,952, and 6,534,273, Weisburg et al.,related to target capture; U.S. Pat. Nos. 5,399,491 and 5,554,516,Kacian et al., related to transcription-mediated amplification; and U.S.Pat. Nos. 5,283,174 and 5,656,744, Arnold et al. and U.S. Pat. No.5,658,737, Nelson et al., related to chemiluminescent labeling anddetection).

In the HPV detection assays described herein, the following reagentswere generally used. Sample Transport Solution contained 15 mM sodiumphosphate monobasic, 15 mM sodium phosphate dibasic, 1 mM EDTA, 1 mMEGTA, and 110 mM lithium lauryl sulfate (LLS), at pH 6.7. Target CaptureReagent contained 250 mM HEPES, 310 mM lithium hydroxide, 1.88 M lithiumchloride, 100 mM EDTA, at pH 6.4, and 250 μg/ml of magnetic particles (1micron SERA-MAG™ MG-CM particles, Seradyn, Inc. Indianapolis, Ind.) with(dT)₁₄ oligomers covalently bound thereto. Wash Solution contained 10 mMHEPES, 150 mM sodium chloride, 6.5 mM sodium hydroxide, 1 mM EDTA, 0.3%(v/v) ethanol, 0.02% (w/v) methyl paraben, 0.01% (w/v) propyl paraben,and 0.1% (w/v) sodium lauryl sulfate, at pH 7.5. Probe Reagent containedone or more labeled detection probes in a solution made up of 100 mMlithium succinate, 2% (w/v) LLS, 15 mM mercaptoethanesulfonate, 1.2 Mlithium chloride, 20 mM EDTA, and 3% (v/v) ethanol, at pH 4.7.Amplification reagent is a concentrated mixture that was mixed withother reaction components to produce a mixture containing 47.6 mMNa-HEPES, 12.5 mM N-acetyl-L-cysteine, 2.5% TRITON™ X-100, 54.8 mM KCl,23 mM MgCl₂, 3 mM NaOH, 0.35 mM of each dNTP (dATP, dCTP, dGTP, dTTP),7.06 mM rATP, 1.35 mM rCTP, 1.35 mM UTP, 8.85 mM rGTP, 0.26 mM Na₂EDTA,5% v/v glycerol, 2.9% trehalose, 0.225% ethanol, 0.075% methylparaben,0.015% propylparaben, and 0.002% Phenol Red, at pH 7.5-7.6, althoughother formulations of amplification reagent may function equally well.Primers may be added to the amplification reagent or added toamplification reactions separate from the amplification reagent. Enzymeswere Moloney Murine Leukemia Virus Reverse Transcriptase (MMLV-RT) andbacteriophage T7 RNA polymerase for which units are functionally definedas: 1 U of MMLV-RT incorporates 1 nmol of dTTP in 10 min at 37° C. using200-400 micromolar oligo dT-primed poly(A) as template, and 1 U of T7RNA polymerase incorporates 1 nmol of ATP into RNA in 1 hr at 37° C.using a DNA template containing a T7 promoter. Hybridization Reagent wasmade up of 100 mM succinic acid, 2% (w/v) LLS, 100 mM lithium hydroxide,15 mM aldrithiol-2, 1.2 M lithium chloride, 20 mM EDTA, and 3.0% (v/v)ethanol, at pH 4.7. Selection Reagent was 600 mM boric acid, 182.5 mMsodium hydroxide, 1% (v/v) octoxynol (TRITON® X-100), at pH 8.5.Detection Reagents were Detect Reagent I, which contained 1 mM nitricacid and 32 mM hydrogen peroxide, and Detect Reagent II was 1.5 M sodiumhydroxide. Oligomers in the HPV assays were generally used in thefollowing concentrations: 2.5 pmol per reaction for each capture probeoligomer, 2.5 pmol per reaction for each promoter primer included intarget capture reagent, 15 pmol per reaction for each non-promoterprimer included in an amplification mixture, 1.25 pmol to 7.5 pmol perreaction of each promoter primer include in an amplification mixtures,and 0.03 pmol per reaction of each detection probe. For the testsperformed, the HPV target generally was a transcript made in vitrocontaining all or part of the E6/E7 gene sequences of the HPV type(s) tobe detected, used at a concentration of 25 to 100,000 copies perreaction, usually at 100 or 1000 copies per reaction. Additional detailsare provided in the examples that follow, which are representative ofsome of the embodiments of the present invention.

EXAMPLE 1 Target Capture, Amplification and Detection of HPV E6/E7Sequences

This example describes assay steps and conditions used in many teststhat detected target sequences from HPV types 16, 18, 31, 33, 35, 39,45, 51, 52, 56, 58, 59, and 68 in a sample.

In the target capture steps, a mixture of oligomers of SEQ ID Nos. 1, 3,5, 7 and 9 (2.5 pmol each) were used in reactions containing 0.5 ml oftarget capture reagent containing 100 or 1,000 copies of HPV target RNAappropriate for each test (i.e., one or more E6/E7 transcripts of HPVtypes 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 68). Thesereaction mixtures also contained 2.5 pmol each of oligomers of SEQ IDNos. 18, 20, 22, 24, 26, 28, 30, 32, 34, and 36. The mixtures wereincubated at 62° C. for 30 min, then at room temperature for 30 min toallow hybridization of the oligomers to the target sequences, then thehybridization complexes on the magnetic particles were separated fromother reaction components by applying magnetic force to the outside ofthe vessel (about 5-10 min), other sample components were aspiratedaway, the hybridization complexes on the particles were washed with 1 mlof wash solution at room temperature and the hybridization complexes onthe magnetic particles were separated from the wash solution by applyingmagnetic force and aspiration as described above.

The captured HPV target RNA in the hybridization complexes that includeat least one T7 promoter primer were then used in amplificationreactions, each containing 40 mM Trizma base, pH 7.5, 17.5 mM KCl, 20 mMMgCl₂, 5% polyvinylpyrrolidone (PVP), 1 mM each dNTP, 4 mM each rNTP,and 15 pmol per reaction each of oligomers of SEQ ID Nos. 38 to 41, andoptimized amounts of the T7 primer oligomers per reaction as follows:SEQ ID NO:18 (1.25 pmol), SEQ ID NO:20 (7.5 pmol), SEQ ID NO:22 (1.25pmol), SEQ ID NO:24 (2.5 pmol), SEQ ID NO:26 (2.5 pmol), SEQ ID NO:28(2.5 pmol), SEQ ID NO:30 (2.5 pmol), SEQ ID NO:32 (7.5 pmol), SEQ IDNO:34 (1.25 pmol), and SEQ ID NO:36 (1.25 pmol). Reactions were coveredwith a layer (200 μl) of inert oil to prevent evaporation, and incubatedat 62° C. for 10-15 min, and then at 42° C. for 3-5 min. Then, enzymes(about 750 U of MMLV RT and about 2000 U of T7 RNA polymerase perreaction) were added, mixed, and the amplification reactions wereincubated at 42° C. for about 1 hr.

For detection of the amplified sequences, 0.1 ml of the probe reagentcontaining a mixture of oligomers of SEQ ID Nos. 11 to 16 or SEQ ID Nos.11 to 15 and17, each at 0.03 pmol per reaction and labeled with AEcompounds, was added to the amplification mixture and incubated at 62°C. for about 20 min, then 0.25 ml of selection reagent was added and themixture was incubated at 62° C. for about 10 min, and then the reactionwas cooled to room temperature (about 15 min) and the chemiluminescencewas produced from bound probes after adding the detection reagents I andII sequentially, substantially as described previously (U.S. Pat. No.5,658,737 at column 25, lines 27-46; Nelson et al., 1996, Biochem.35:8429-8438 at 8432), and the signals (relative light units or RLU)were detected (for 2 sec) by using a luminometer (Leader HC+, Gen-ProbeInc., San Diego, Calif.).

In a series of multiplex assays, target sequences of HPV types 16, 18,31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 68 were each amplified anddetected using the assays described above using samples containing knownamounts of each target (in a range of 25 to 1000 copies per reaction).All of the HPV types provided positive signals, generally in a range ofabout 650,000 RLU to over 2,000,000 RLU for samples that contained 200or more copies of each of the target HPV RNA, although HPV types 31, 35,18, 45, 59, and 68 provided positive signals (greater than 500,000 RLU)when as few as 25 copies of the target RNA was present in the sample.Based on the results, the approximate sensitivity of the multiplex assaywas 25 copies per reaction for HPVs 18, 31, 35, 45, 51, 56, 59 and 68,50 copies per reaction for HPV16, 200 copies per reaction for HPVs 33,39 and 58, and 400 copies per reaction for HPV52.

To show that the multiplex assay did not cross react with HPV types thatthe assay was not designed to detect, i.e., low risk HPV types, the samemultiple amplification and detection reaction steps were performed usingas the target nucleic acids in vitro E6/E7 transcripts made from lowrisk HPV types 6, 11, 42, 43 and 44, used at 1,000,000 and 10,000,000copies per reaction. That is, the low risk HPV types were tested at1,000-fold to 10,000-fold more copies per reaction than for thehigh-risk HPV types of groups A1, A2, C1, C2, and D that the assaydetected. The low risk HPV targets tested in the assay provided negativeresults compared to the positive controls (1000 copies of HPV16, 18, 33,39 and 51 in vitro E6/E7 transcripts tested in individual reactions foreach target HPV). The positive controls provided positive signals ofgreater than 1,000,000 to greater than 2,000,000 RLU, while the low riskHPV types provided negative signals (about 14,000 RLU or less).

EXAMPLE 2 Amplification and Detection of HPV Types in Groups A2, C1, C2and D

This example presents some of the tests done to demonstrateamplification and detection of individual HPV types in different groupsusing combinations of amplification and detection oligomers. Thereactions were performed substantially as described above, using onlyamplification and detection steps to the efficiency of detecting targetsequences in test samples that were made using known amounts of in vitrotranscripts of the E7 regions (100 to 100,000 copies per reaction).Negative controls were samples tested identically but containing notarget transcripts. Amplification reactions were performed individuallyfor each group using the same amounts per reaction of each non-promoterprimer (15 pmol) and each promoter primer (5 to 7.5 pmol) tested in thereactions for that group (shown by their SEQ ID NOs with the data tablesthat follow). The prepared samples containing known amounts of each HPVtarget RNA were mixed with amplification reagents (40 mM Trizma base, pH7.5, 17.5 mM KCl, 20 mM MgCl₂, 5% polyvinylpyrrolidone (PVP), 1 mM eachdNTP, 4 mM each rNTP) and each the amplification oligomers shown in thedata tables that follow for each group. Reactions were covered with alayer of inert oil to prevent evaporation, incubated at 62° C. for 10-15min, then at 42° C. for 3-5 min, and then enzymes (about 750 U of MMLVRT and about 2000 U of T7 RNA polymerase per reaction) were added,mixed, and the amplification reactions were incubated at 42° C. forabout 1 hr. Following amplification, an aliquot of each of theamplification reactions was mixed with hybridization reagent andAE-labeled probes (100 fmol per reaction) of the sequences shown for thedata tables that follow for each group, and the mixtures were incubatedto allow hybridization of the probes to the amplified products (62° C.for about 20 min) and then selection reagent was added to inactivate thelabel on unbound probes (at 62° C. for about 10 min). The detectionreaction mixtures were cooled to room temperature, Detect Reagents I andII were added sequentially to induce chemiluminescence from boundprobes, and the chemiluminescent signals (RLU) were detected in ailluminometer substantially as described previously (U.S. Pat. No.5,658,737; Nelson et al., 1996, Biochem. 35:8429-8438 at 8432). Theresults of tests for the HPV types of groups A2, C1, C2 and D are shownbelow.

TABLE 2 Group A2 Types: RLU Detected Following Amplification andDetection with Probe of SEQ ID NO: 12 Target Copies Per Reaction PrimersHPV 0 100 1,000 10,000 100,000 targets HPV33 3,438 7,900,599 7,850,9858,184,822 8,006,992 24, 38 3,035 18,198 91,184 2,448,776 6,805,674 26,38 3,962 7,870,920 7,875,748 7,768,868 7,778,976 24, 26, 38 HPV58 5,52010,386,537 10,413,923 10,593,322 10,651,717 24, 38 4,656 13,533 21,115129,118 1,021,726 26, 38 2,945 5,002,410 5,429,599 5,637,786 5,743,31024, 26, 38

TABLE 3 Group C1 Types: RLU Detected Following Amplification andDetection Target Copies Per Reaction Primers/Probes HPV 0 100 1,00010,000 100,000 targets HPV45 5,502 2,288,692 8,243,285 10,191,40110,036,303 28, 39/47 HPV18 2,155 766,270 2,638,578 6,766,617 6,841,98028, 39/44

TABLE 4 Group C2 Types: RLU Detected Following Amplification andDetection with Probe of SEQ ID NO: 14 Target Copies Per Reaction PrimersHPV 0 100 1,000 10,000 100,000 targets HPV39 5,793 9,782,945 9,771,5889,784,294 9,432,972 32, 40 HPV68 6,996 8,398,120 9,389,473 9,509,9429,472,284 32, 40

TABLE 5 Group D Types: RLU Detected Following Amplification andDetection Target Copies Per Reaction Primers/Probes HPV 0 100 1,00010,000 100,000 targets HPV51 7,157 7,199,400 8,956,784 9,128,5679,100,401 34, 36, 41/15 7,476 7,626,000 8,971,061 8,962,289 9,083,18834, 41/15 7,953 6,352,096 7,188,431 7,247,835 7,258,649 34, 36, 41/15,16 8,719 5,148,663 7,132,653 7,328,616 6,527,860 34, 41/15, 16 HPV562,342 4,143,796 5,096,028 5,266,208 5,248,864 34, 36, 41/16 3,2634,975,678 5,050,576 5,245,685 5,242,688 34, 41/16These results show that the selected oligomers are effective atamplification and detection of different HPV types within a group, oftenproviding positive results with as few as 100 copies per reaction of thetarget RNA. Many similar tests were performed using other combinationsof amplification and detection oligomers disclosed herein with theirrespective HPV target transcripts which also provided positive resultswith as few as 100 copies of target RNA per reaction and consistentlyprovided positive results when 1000 copies of target RNA per reaction.

EXAMPLE 3 Multiplex Assay to Amplify and Detect HPV Types of Groups A1,A2, C1, C2 and D

This example shows results obtained with a multiplex assay similar tothat described in Example 1 that detected HPV types 16, 18, 31, 33, 35,39, 45, 51, 52, 56, 58, 59, 68. This multiplex assay further included aninternal control (IC) RNA (a randomized non-HPV RNA sequence) that wassimultaneously amplified and detected by using IC-specific primers andprobe, to produce a distinguishable chemiluminescent signal underidentical assay conditions as used to detect the HPV analytes.

In the target capture portion of the assay, a mixture of captureoligomers of SEQ ID NO:1 (0.65 pmol/μl) SEQ ID NO:3 and SEQ ID NO:9 (2.5pmol/μl each), and SEQ ID NO:5 and SEQ ID NO:7 (0.5 pmol/μl each) wereused in reactions containing target capture reagent and samplescontaining a known amount of HPV target RNA (in vitro transcripts of theE6/E7 gene region of HPV type 16, 18, 31, 33, 35, 39, 45, 51, 52, 56,58, 59, or 68 at 100 to 1,000 copies per reaction). The capture reactionmixtures were incubated sequentially at 62° C. for 30 min and roomtemperature for 30 min to allow formation of hybridization complexesmade up of HPV RNA:capture oligomer:immobilized probe on the solidsupport particles. The hybridization complexes on the particles wereseparated from other sample components by applying magnetic force to theoutside of the vessel, aspirating other sample components away, andwashing the hybridization complexes on the particles substantially asdescribed above.

The captured HPV target RNA in the hybridization complexes were thenamplified in a transcription mediated amplification reaction thatincluded amplification reagent and amplification oligomers provided tothe reaction from a mixture of promoter primers and a mixture ofnon-promoter primers. The promoter primers used were those of SEQ IDNO:18 (1.25 pmol/μl), SEQ ID NO:20 (7.5 pmol/μl), SEQ ID NO:22 (1.25pmol/μl), SEQ ID NO:24 (7.5 pmol/μl), SEQ ID NO:26 (7.5 pmol/μl), SEQ IDNO:28 (2.5 pmol/μl), SEQ ID NO:30 (2.5 pmol/μl), SEQ ID NO:32 (7.5pmol/μl), SEQ ID NO:34 (1.25 pmol/μl), and SEQ ID NO:36 (1.25 pmol/μl).The other primers were those of SEQ ID Nos. 38, 39, 40 and 41 (each at15 pmol/μl). A promoter primer and primer specific for the internalcontrol were also added to reactions that contained the internal controlRNA. The mixtures were covered with a layer of inert oil to preventevaporation, incubated sequentially at 62° C. for 10-15 min and 42° C.for about 5 min. Enzymes (MMLV RT and T7 RNA polymerase) were added,mixed, and the amplification reactions were incubated at 42° C. forabout 60 min (45 to 75 min) substantially as described above.

For detection of the amplified HPV sequences, an aliquot of theamplification mixture was mixed with probe reagent and a mixture ofprobe oligomers of SEQ ID Nos. 11, 12, 14, 15, 17, 44, 45 and 52, eachlabeled with 2-methyl-AE and added in amounts to provide 1.5×10⁶ RLU perreaction. Detection of the amplified internal control sequences used asynthetic oligomer specific for the internal control and labeled with adistinguishable AE compound (2′-fluoro-AE), added in an amount toprovide 8.5×10⁵ RLU per reaction. The detection mixtures were incubatedat 62° C. for about 20 min, then cooled at room temperature for about 5min, and selection reagent was added and the mixture was incubated at62° C. for about 10 min, and then cooled to room temperature for about15 min, when chemiluminescence was produced by using detection reagentsI and II sequentially, and chemiluminescent signals (RLU) from the AElabels in bound probes were detected substantially as described above.

In these assays, a total of 10 replicate samples were tested for each ofthe HPV targets and copy numbers assayed, for which representative datais presented below for two different lots of amplification reagentsused. The average RLU (mean) detected for the amplified target HPVsequences by type of the replicate reactions are shown along with thepercentage of tests that were considered positive based on the detectedRLU above background levels obtained in samples that contained no HPVtarget RNA that were treated identically. The results show that themultiplex assay detects HPV types 16, 18, 31, 33, 35, 39, 45, 51, 52,56, 58, 59 and 68, although some variation in the results was observed(e.g., between individual specimens, performance of individual assays,or reagent lots). These results also show the relative sensitivity ofthe assay for the different HPV types tested.

TABLE 6 Copies/ Detected RLU HPV Type reaction (mean) % Positive (n =10) Reagent Lot 16 100 961,914 100 1 31 250 855,243 100 1 31 100 872,710100 1 35 100 1,004,241 100 1 33 100 904,880 100 1 16 100 1,032,372 100 231 250 1,037,532 100 2 31 100 860,320 100 2 35 100 1,036,048 100 2 33100 303,667 90 2 52 100 569,196 50 1 58 100 872,453 100 1 18 1000526,424 100 1 18 500 383,899 90 1 56 250 736,253 100 1 52 100 26,251 0 258 100 184,647 60 2 18 1000 562,169 90 2 18 500 324,432 70 2 56 250899,826 100 2 16 100 863,950 100 1 45 1000 100,368 20 1 45 500 43,731 101 59 1000 613,100 90 1 59 500 367,401 90 1 45 1000 382,050 100 2 45 500264,810 100 2 59 1000 739,276 100 2 59 500 716,386 100 2 39 1001,154,632 100 1 68 500 965,785 100 1 51 250 351,527 100 1 51 100 281,80670 1 56 100 369,690 90 1 39 100 545,835 90 2 68 500 271,722 100 2 51 250431,593 100 2 51 100 229,267 80 2 56 100 664,674 100 2

The above examples illustrate aspects and preferred embodiments of theinvention which is claimed below.

1-20. (canceled)
 21. A mixture of oligomers for detecting multiple typesof human papillomavirus (HPV) nucleic acids, wherein the mixtureincludes first amplification oligomers, comprising a target bindingregion and a 5′ promoter sequence, and second amplification oligomers,comprising a target binding region, wherein pairs of the first andsecond amplification oligomers hybridize to opposing strands of HPVnucleic acids for transcription mediated amplification of HPV nucleicacids between pairs of hybridized first and second amplificationoligomers, wherein: (a) the first amplification oligomers comprisenucleic acid sequences selected from the group consisting of SEQ ID Nos.18, 20, 22, 24, 28, 30, 32, 34, 36, RNA equivalents thereof, complementsthereof, and combinations thereof; and (b) the second amplificationoligomers comprise nucleic acid sequences selected from the groupconsisting of SEQ ID Nos. 38, 39, 40, 41, RNA equivalents thereof,complements thereof, and combinations thereof.
 22. The mixture ofoligomers of claim 21, in which one or more individual oligomerscomprises at least one 2′-methoxy RNA group, at least one 2′fluoro-substituted RNA group, at least one peptide nucleic acid linkage,at least one phosphorothioate linkage, at least one methylphosphonatelinkage or any combination thereof.
 23. The mixture of oligomers ofclaim 21 contained in a kit.
 24. The mixture of oligomers of claim 21,further comprising at least two detection probe oligomers comprisingsequences selected from the group consisting of SEQ ID NO:11 to SEQ IDNO:17, SEQ ID NO:44 to SEQ ID NO:54 and SEQ ID NO:58, which includes thecomplementary oligomer sequences or RNA equivalents of the specifiedsequences.
 25. The mixture of oligomers of claim 24, wherein eacholigomer sequence includes a label joined directly or indirectly to theoligomer.
 26. The mixture of oligomers of claim 24, wherein eacholigomer sequence includes a label that is a chemiluminescent compound.27. The mixture of oligomers of claim 24, wherein each oligomer sequencehas a backbone comprising at least one 2′-methoxy RNA group.
 28. Themixture of claim 21, wherein the first amplification oligomers are atleast three amplification oligomers comprising nucleic acid sequencesselected from the group consisting of SEQ ID Nos. 18, 20, 22, 24, 28,30, 32, 34, 36, RNA equivalents thereof, complements thereof, andcombinations thereof and the second amplification oligomers are at leastthree amplification oligomers comprising nucleic acid sequences selectedfrom the group consisting of SEQ ID Nos. 38, 39, 40, 41, RNA equivalentsthereof, complements thereof, and combinations thereof.
 29. The mixtureof at least two oligomers of claim 21, further comprising at least twocapture oligomers selected from SEQ ID Nos. 2, 4, 6, 8 and 10 with aligand moiety joined to each oligomer, and SEQ ID Nos. 1, 3, 5, 7 and 9,including RNA equivalents thereof, complements thereof, and combinationsthereof.
 30. The mixture of oligomers of claim 29, wherein at least oneoligomer comprises at least one 2′-methoxy RNA group, at least one 2′fluoro-substituted RNA group, at least one peptide nucleic acid linkage,at least one phosphorothioate linkage, or at least one methylphosphonatelinkage.
 31. The mixture of oligomers of claim 29 contained in a kit.